rs4561
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001118890.2(GLRX):āc.225T>Cā(p.Ile75=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 1,580,096 control chromosomes in the GnomAD database, including 125,296 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.37 ( 10776 hom., cov: 31)
Exomes š: 0.40 ( 114520 hom. )
Consequence
GLRX
NM_001118890.2 synonymous
NM_001118890.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.15
Genes affected
GLRX (HGNC:4330): (glutaredoxin) This gene encodes a member of the glutaredoxin family. The encoded protein is a cytoplasmic enzyme catalyzing the reversible reduction of glutathione-protein mixed disulfides. This enzyme highly contributes to the antioxidant defense system. It is crucial for several signalling pathways by controlling the S-glutathionylation status of signalling mediators. It is involved in beta-amyloid toxicity and Alzheimer's disease. Multiple alternatively spliced transcript variants encoding the same protein have been identified. [provided by RefSeq, Aug 2011]
RHOBTB3 (HGNC:18757): (Rho related BTB domain containing 3) Enables ATP binding activity and small GTPase binding activity. Involved in retrograde transport, endosome to Golgi. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP7
?
Synonymous conserved (PhyloP=-1.14 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLRX | NM_001118890.2 | c.225T>C | p.Ile75= | synonymous_variant | 2/3 | ENST00000237858.11 | |
GLRX | NM_001243658.2 | c.225T>C | p.Ile75= | synonymous_variant | 2/3 | ||
GLRX | NM_001243659.2 | c.225T>C | p.Ile75= | synonymous_variant | 2/3 | ||
GLRX | NM_002064.3 | c.225T>C | p.Ile75= | synonymous_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLRX | ENST00000237858.11 | c.225T>C | p.Ile75= | synonymous_variant | 2/3 | 1 | NM_001118890.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.371 AC: 56350AN: 151844Hom.: 10779 Cov.: 31
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GnomAD3 exomes AF: 0.363 AC: 91306AN: 251296Hom.: 17568 AF XY: 0.373 AC XY: 50684AN XY: 135826
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GnomAD4 exome AF: 0.395 AC: 564812AN: 1428134Hom.: 114520 Cov.: 26 AF XY: 0.397 AC XY: 282892AN XY: 712506
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GnomAD4 genome ? AF: 0.371 AC: 56369AN: 151962Hom.: 10776 Cov.: 31 AF XY: 0.367 AC XY: 27291AN XY: 74266
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at